Merge pull request #152 from ga4gh/reorganize-spec-content

explode out openapi spec to use multifile organization

Author: jaeddy

openapi/components/schemas/DefaultWorkflowEngineParameter.yaml

@@ -0,0 +1,13 @@
+title: DefaultWorkflowEngineParameter
+type: object
+properties:
+  name:
+    type: string
+    description: The name of the parameter
+  type:
+    type: string
+    description: Describes the type of the parameter, e.g. float.
+  default_value:
+    type: string
+    description: The stringified version of the default parameter. e.g. "2.45".
+description: A message that allows one to describe default parameters for a workflow engine.

openapi/components/schemas/ErrorResponse.yaml

@@ -0,0 +1,11 @@
+title: ErrorResponse
+type: object
+properties:
+  msg:
+    type: string
+    description: A detailed error message.
+  status_code:
+    type: integer
+    description: The integer representing the HTTP status code (e.g. 200, 404).
+    format: int32
+description: An object that can optionally include information about the error.

openapi/components/schemas/Log.yaml

@@ -0,0 +1,28 @@
+title: Log
+type: object
+properties:
+  name:
+    type: string
+    description: The task or workflow name
+  cmd:
+    type: array
+    items:
+      type: string
+    description: The command line that was executed
+  start_time:
+    type: string
+    description: When the command started executing, in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
+  end_time:
+    type: string
+    description: When the command stopped executing (completed, failed, or cancelled), in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
+  stdout:
+    type: string
+    description: A URL to retrieve standard output logs of the workflow run or task.  This URL may change between status requests, or may not be available until the task or workflow has finished execution.  Should be available using the same credentials used to access the WES endpoint.
+  stderr:
+    type: string
+    description: A URL to retrieve standard error logs of the workflow run or task.  This URL may change between status requests, or may not be available until the task or workflow has finished execution.  Should be available using the same credentials used to access the WES endpoint.
+  exit_code:
+    type: integer
+    description: Exit code of the program
+    format: int32
+description: Log and other info

openapi/components/schemas/RunId.yaml

@@ -0,0 +1,6 @@
+title: RunId
+type: object
+properties:
+  run_id:
+    type: string
+    description: workflow run ID

openapi/components/schemas/RunListResponse.yaml

@@ -0,0 +1,12 @@
+title: RunListResponse
+type: object
+properties:
+  runs:
+    type: array
+    items:
+      $ref: './RunStatus.yaml'
+    description: A list of workflow runs that the service has executed or is executing. The list is filtered to only include runs that the caller has permission to see.
+  next_page_token:
+    type: string
+    description: A token which may be supplied as `page_token` in workflow run list request to get the next page of results.  An empty string indicates there are no more items to return.
+description: The service will return a RunListResponse when receiving a successful RunListRequest.

openapi/components/schemas/RunLog.yaml

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+title: RunLog
+type: object
+properties:
+  run_id:
+    type: string
+    description: workflow run ID
+  request:
+    $ref: './RunRequest.yaml'
+  state:
+    $ref: './State.yaml'
+  run_log:
+    $ref: './Log.yaml'
+  task_logs:
+    type: array
+    items:
+      $ref: './Log.yaml'
+    description: The logs, and other key info like timing and exit code, for each step in the workflow run.
+  outputs:
+    type: object
+    description: The outputs from the workflow run.

openapi/components/schemas/RunRequest.yaml

@@ -0,0 +1,39 @@
+title: RunRequest
+type: object
+properties:
+  workflow_params:
+    type: object
+    description: >-
+      REQUIRED
+
+      The workflow run parameterizations (JSON encoded), including input and output file locations
+  workflow_type:
+    type: string
+    description: >-
+      REQUIRED
+
+      The workflow descriptor type, must be "CWL" or "WDL" currently (or another alternative supported by this WES instance)
+  workflow_type_version:
+    type: string
+    description: >-
+      REQUIRED
+
+      The workflow descriptor type version, must be one supported by this WES instance
+  tags:
+    type: object
+    additionalProperties:
+      type: string
+  workflow_engine_parameters:
+    type: object
+    additionalProperties:
+      type: string
+  workflow_url:
+    type: string
+    description: >-
+      REQUIRED
+
+      The workflow CWL or WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.
+description: >-
+  To execute a workflow, send a run request including all the details needed to begin downloading
+
+  and executing a given workflow.

openapi/components/schemas/RunStatus.yaml

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+title: RunStatus
+required:
+- run_id
+type: object
+properties:
+  run_id:
+    type: string
+  state:
+    $ref: './State.yaml'
+description: Small description of a workflow run, returned by server during listing

openapi/components/schemas/ServiceInfo.yaml

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+title: ServiceInfo
+allOf:
+  - $ref: 'https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/v1.0.0/service-info.yaml#/components/schemas/Service'
+  - type: object
+    properties:
+      workflow_type_versions:
+        type: object
+        additionalProperties:
+          $ref: './WorkflowTypeVersion.yaml'
+      supported_wes_versions:
+        type: array
+        items:
+          type: string
+        description: The version(s) of the WES schema supported by this service
+      supported_filesystem_protocols:
+        type: array
+        items:
+          type: string
+        description: The filesystem protocols supported by this service, currently these may include common protocols using the terms 'http', 'https', 'sftp', 's3', 'gs', 'file', or 'synapse', but others  are possible and the terms beyond these core protocols are currently not fixed.   This section reports those protocols (either common or not) supported by this WES service.
+      workflow_engine_versions:
+        type: object
+        additionalProperties:
+          type: string
+      default_workflow_engine_parameters:
+        type: array
+        items:
+          $ref: './DefaultWorkflowEngineParameter.yaml'
+        description: Each workflow engine can present additional parameters that can be sent to the workflow engine. This message will list the default values, and their types for each workflow engine.
+      system_state_counts:
+        type: object
+        additionalProperties:
+          type: integer
+          format: int64
+      auth_instructions_url:
+        type: string
+        description: A web page URL with human-readable instructions on how to get an authorization token for use with a specific WES endpoint.
+      tags:
+        type: object
+        additionalProperties:
+          type: string
+          description: A message containing useful information about the running service, including supported versions and default settings.
+      required:
+        - workflow_type_versions
+        - supported_wes_versions
+        - supported_filesystem_protocols
+        - workflow_engine_versions
+        - default_workflow_engine_parameters
+        - system_state_counts
+        - auth_instructions_url
+        - tags

openapi/components/schemas/State.yaml

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+title: State
+enum:
+- UNKNOWN
+- QUEUED
+- INITIALIZING
+- RUNNING
+- PAUSED
+- COMPLETE
+- EXECUTOR_ERROR
+- SYSTEM_ERROR
+- CANCELED
+- CANCELING
+type: string
+description: >
+  State can take any of the following values:
+
+    + UNKNOWN: The state of the task is unknown. This provides a safe default for messages where this field is missing, for example, so that a missing field does not accidentally imply that the state is QUEUED.
+
+    + QUEUED: The task is queued.
+
+    + INITIALIZING: The task has been assigned to a worker and is currently preparing to run. For example, the worker may be turning on, downloading input files, etc.
+
+    + RUNNING: The task is running. Input files are downloaded and the first Executor has been started.
+
+    + PAUSED: The task is paused. An implementation may have the ability to pause a task, but this is not required.
+
+    + COMPLETE: The task has completed running. Executors have exited without error
+    and output files have been successfully uploaded.
+
+    + EXECUTOR_ERROR: The task encountered an error in one of the Executor processes. Generally,
+  this means that an Executor exited with a non-zero exit code.
+
+    + SYSTEM_ERROR: The task was stopped due to a system error, but not from an Executor,
+  for example an upload failed due to network issues, the worker's ran out of disk space, etc.
+
+    + CANCELED: The task was canceled by the user.
+
+    + CANCELING: The task was canceled by the user, and is in the process of stopping.